| geneColor |
Class "GeneColorSet" |
| geneColor,GeneColorSet-method |
Class "GeneColorSet" |
| geneColor<-,GeneColorSet,factor-method |
Class "GeneColorSet" |
| GeneColorSet |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,BroadCollection-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,character-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,ExpressionSet-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,GeneIdentifierType-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,GeneSet-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,GOCollection-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet,missing-method |
Methods to Construct "GeneColorSet" Instances |
| GeneColorSet-class |
Class "GeneColorSet" |
| GeneColorSet-methods |
Methods to Construct "GeneColorSet" Instances |
| GeneIdentifierType |
Gene Identifier Class Constructors |
| GeneIdentifierType-class |
Class "GeneIdentifierType" |
| geneIds |
Class "GeneSet" |
| geneIds,GeneSet-method |
Class "GeneSet" |
| geneIds,GeneSetCollection-method |
Class "GeneSetCollection" |
| geneIds<-,GeneSet,character-method |
Class "GeneSet" |
| geneIds<-,GeneSetCollection,list-method |
Class "GeneSetCollection" |
| geneIdType |
Class "GeneSet" |
| geneIdType,GeneIdentifierType-method |
Class "GeneIdentifierType" |
| geneIdType,GeneSet-method |
Class "GeneSet" |
| geneIdType<-,GeneSet,character-method |
Class "GeneSet" |
| geneIdType<-,GeneSet,GeneIdentifierType-method |
Class "GeneSet" |
| GenenameIdentifier |
Gene Identifier Class Constructors |
| GenenameIdentifier-class |
Class "GeneIdentifierType" |
| GeneSet |
Methods to construct GeneSet instances |
| GeneSet,BroadCollection-method |
Methods to construct GeneSet instances |
| GeneSet,character-method |
Methods to construct GeneSet instances |
| GeneSet,ExpressionSet-method |
Methods to construct GeneSet instances |
| GeneSet,GeneIdentifierType-method |
Methods to construct GeneSet instances |
| GeneSet,GOCollection-method |
Methods to construct GeneSet instances |
| GeneSet,missing-method |
Methods to construct GeneSet instances |
| GeneSet-class |
Class "GeneSet" |
| GeneSet-methods |
Methods to construct GeneSet instances |
| GeneSetCollection |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,character,AnnotationIdentifier,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,character,AnnotationIdentifier,CollectionType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,ExpressionSet,missing,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,ExpressionSet,missing,CollectionType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,ExpressionSet,missing,GOCollection-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,ExpressionSet,missing,KEGGCollection-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,GeneSet,missing,missing-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,list,missing,missing-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,missing,AnnotationIdentifier,CollectionType-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,missing,AnnotationIdentifier,GOCollection-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-method |
Methods to construct GeneSetCollection instances |
| GeneSetCollection-class |
Class "GeneSetCollection" |
| GeneSetCollection-methods |
Methods to construct GeneSetCollection instances |
| getBroadSets |
Read and write gene sets from Broad or GMT formats |
| getGmt |
Read and write gene sets from Broad or GMT formats |
| getOBOCollection |
Read OBO-specified Gene Ontology Collections |
| GOCollection |
Collection Type Class Constructors |
| GOCollection-class |
Class "CollectionType" |
| goIds |
Class "CollectionType" |
| goIds,GOCollection-method |
Class "CollectionType" |
| goSlim |
Methods for Function goSlim in Package ‘GSEABase’ |
| goSlim,ExpressionSet,GOCollection-method |
Methods for Function goSlim in Package ‘GSEABase’ |
| goSlim,GOCollection,GOCollection-method |
Methods for Function goSlim in Package ‘GSEABase’ |
| goSlim-methods |
Methods for Function goSlim in Package ‘GSEABase’ |
| GSEABase |
Gene set enrichment data structures and methods |
| ids |
Class "CollectionType" |
| ids,CollectionIdType-method |
Class "CollectionType" |
| incidence |
Methods for Constructing Incidence Matricies Between GeneSets |
| incidence,GeneSet-method |
Methods for Constructing Incidence Matricies Between GeneSets |
| incidence,GeneSetCollection-method |
Methods for Constructing Incidence Matricies Between GeneSets |
| incidence-methods |
Methods for Constructing Incidence Matricies Between GeneSets |
| initialize,GeneColorSet-method |
Class "GeneColorSet" |
| initialize,GeneIdentifierType-method |
Class "GeneIdentifierType" |
| initialize,GeneSet-method |
Class "GeneSet" |
| intersect,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
| intersect,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
| intersect,CollectionType,CollectionType-method |
Class "CollectionType" |
| intersect,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
| intersect,GeneSet,GeneSet-method |
Class "GeneSet" |
| intersect,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
| io |
Read and write gene sets from Broad or GMT formats |
| MapCollection |
Collection Type Class Constructors |
| MapCollection-class |
Class "CollectionType" |
| mapIdentifiers |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,ANY,ANY,ANY-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneColorSet,NullIdentifier,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,GeneIdentifierType,AnnDbBimap-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,GeneIdentifierType,environment-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,GeneIdentifierType,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,GeneIdentifierType,missing-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,GeneIdentifierType,NullIdentifier-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSet,NullIdentifier,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers,GeneSetCollection,GeneIdentifierType,missing-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| mapIdentifiers-methods |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
| setdiff,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
| setdiff,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
| setdiff,CollectionType,CollectionType-method |
Class "CollectionType" |
| setdiff,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
| setdiff,GeneSet,GeneSet-method |
Class "GeneSet" |
| setdiff,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
| setIdentifier |
Class "GeneSet" |
| setIdentifier,GeneSet-method |
Class "GeneSet" |
| setIdentifier<-,GeneSet,character-method |
Class "GeneSet" |
| setName |
Class "GeneSet" |
| setName,GeneSet-method |
Class "GeneSet" |
| setName<-,GeneSet,character-method |
Class "GeneSet" |
| setVersion |
Class "GeneSet" |
| setVersion,GeneSet-method |
Class "GeneSet" |
| setVersion<-,GeneSet,Versions-method |
Class "GeneSet" |
| show,AnnotationIdentifier-method |
Class "GeneIdentifierType" |
| show,BroadCollection-method |
Class "CollectionType" |
| show,CollectionIdType-method |
Class "CollectionType" |
| show,CollectionType-method |
Class "CollectionType" |
| show,GeneColorSet-method |
Class "GeneColorSet" |
| show,GeneIdentifierType-method |
Class "GeneIdentifierType" |
| show,GeneSet-method |
Class "GeneSet" |
| show,GeneSetCollection-method |
Class "GeneSetCollection" |
| show,GOCollection-method |
Class "CollectionType" |
| show,OBOCollection-method |
Class "OBOCollection" |
| subsets |
Class "OBOCollection" |
| subsets,OBOCollection-method |
Class "OBOCollection" |
| SymbolIdentifier |
Gene Identifier Class Constructors |
| SymbolIdentifier-class |
Class "GeneIdentifierType" |
| [,CollectionIdType,missing,missing-method |
Class "CollectionType" |
| [,ExpressionSet,GeneSet,ANY-method |
Class "GeneSet" |
| [,GeneColorSet,character,ANY-method |
Class "GeneColorSet" |
| [,GeneColorSet,numeric,ANY-method |
Class "GeneColorSet" |
| [,GeneSet,character,ANY-method |
Class "GeneSet" |
| [,GeneSet,numeric,ANY-method |
Class "GeneSet" |
| [,GeneSetCollection,character,ANY-method |
Class "GeneSetCollection" |
| [,GeneSetCollection,logical,ANY-method |
Class "GeneSetCollection" |
| [,GeneSetCollection,numeric,ANY-method |
Class "GeneSetCollection" |
| [,GOCollection,missing,missing-method |
Class "CollectionType" |
| [,OBOCollection,character,missing-method |
Class "OBOCollection" |
| [<-,GeneSetCollection,ANY,ANY,ANY-method |
Class "GeneSetCollection" |
| [<-,GeneSetCollection,ANY,ANY,GeneSet-method |
Class "GeneSetCollection" |
| [<-,GeneSetCollection,character,ANY,GeneSet-method |
Class "GeneSetCollection" |
| [[,GeneColorSet,character-method |
Class "GeneColorSet" |
| [[,GeneColorSet,numeric-method |
Class "GeneColorSet" |
| [[,GeneSet,character-method |
Class "GeneSet" |
| [[,GeneSet,numeric-method |
Class "GeneSet" |
| [[,GeneSetCollection,character-method |
Class "GeneSetCollection" |
| [[<-,GeneSetCollection,ANY,ANY,ANY-method |
Class "GeneSetCollection" |
| [[<-,GeneSetCollection,character,ANY,GeneSet-method |
Class "GeneSetCollection" |
| [[<-,GeneSetCollection,numeric,ANY,GeneSet-method |
Class "GeneSetCollection" |
| |,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
| |,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
| |,CollectionType,CollectionType-method |
Class "CollectionType" |
| |,GeneColorSet,character-method |
Class "GeneColorSet" |
| |,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
| |,GeneSet,character-method |
Class "GeneSet" |
| |,GeneSet,GeneSet-method |
Class "GeneSet" |
| |,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
| |,GeneSetCollection,GeneSetCollection-method |
Class "GeneSetCollection" |